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Occurrence of virulence genes, 16S rRNA methylases, and plasmid-mediated quinolone resistance genes in CTX-M-producing Escherichia coli from Pakistan

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Abstract

The aim of the study was to conduct a comprehensive molecular characterization of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli collected from Pakistan. Genetic relatedness among 98 ESBL-producing E. coli was measured by pulsed-field gel electrophoresis (PFGE). The presence of genes encoding ESBLs, virulence factors (VFs), 16S rRNA methylases, plasmid-mediated quinolone resistance (PMQR) encoding elements, plasmid replicon types, phylogenetic groups of E. coli, prevalence of the worldwide disseminated clone E. coli ST131, and phylogrouping of CTX-M enzymes was investigated by polymerase chain reaction (PCR). All isolates carried bla CTX-M genes and, except for one isolate from CTX-M phylogroup 9, they all belonged to CTX-M phylogroup 1. The isolates were genetically diverse with PFGE. Phylogenetic group D (36 %) was most abundant in this collection of E. coli, whereas isolates belonging to B2 (22 %) had the highest content of virulence genes. PMQR genes were found in 84.6 % of the isolates; among them, 93 % isolates were positive for variants of acetyltransferases (aac(6′)-lb-cr), whereas qnrB, qepA, and qnrS were present in 11 %, 5 %, and 4 % of the isolates, respectively. Only 3 % of the isolates contained genes encoding 16S rRNA methylases. The most abundant replicon type was IncF (96 %), and 18 % of the isolates belonged to the ST131 clone. Out of 34 investigated VFs, 24 genes encoding different types of adhesins, protectins, toxins, siderophores, and other VFs were found. Although the isolates in this collection were highly resistant to many antimicrobials, susceptibility to amikacin and meropenem was retained.

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan

    M. A. Habeeb & A. Haque

  2. Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan

    M. A. Habeeb & A. Haque

  3. Clinical Microbiology L2:02, Karolinska Institutet—MTC, Karolinska University Hospital Solna, 17176, Stockholm, Sweden

    M. A. Habeeb, A. Iversen & C. G. Giske

  4. Institute of Molecular Biology and Biotechnology, The University of Lahore, Defense Road, Lahore, Pakistan

    M. A. Habeeb

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  1. M. A. Habeeb
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  2. A. Haque
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  4. C. G. Giske
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Correspondence to C. G. Giske.

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Habeeb, M.A., Haque, A., Iversen, A. et al. Occurrence of virulence genes, 16S rRNA methylases, and plasmid-mediated quinolone resistance genes in CTX-M-producing Escherichia coli from Pakistan. Eur J Clin Microbiol Infect Dis 33, 399–409 (2014). https://doi.org/10.1007/s10096-013-1970-1

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  • DOI: https://doi.org/10.1007/s10096-013-1970-1

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